Taoiseach has told the Fianna Fáil parliamentary party that he will meet individual TDs and Senators to discuss the outcome of the local land European elections.
However, he stressed that the party would work to reorganise ahead of the next General Election in three years time.
Over 90 TDs and Senators attended this four-and-a-half hour post mortem that heard some three dozen speakers.
Mr Cowen opened the meeting with a frank assessment of the election performance. He said the party would now begin a three-year process of reorganisation ahead of the next General Election.
There had been similar exercises under Sean Lemass and Jack Lynch, he told the meeting.
Afterwards Government Chief Whip Pat Carey said a priority would be modernising the party in Dublin to make Fianna Fáil a campaigning organisation again.
It would amount to a radical overhaul that would make the party fit for purpose. Fianna Fáil, he said, was down but not out.
Some speakers raised the question of a reshuffle of ministers but the main thrust appears to have been shortcomings in party organisation.
With both the Greens and Fianna Fáil closing ranks after disastrous elections results there was no open criticism of the leadership.
Earlier, the Taoiseach rejected calls from the leaders of the Opposition to call a General Election.
Mr Cowen said the Government's mandate ran up to 2012 and dismissed suggestions to the contrary as 'disingenuous'.
He said the people are fed up with the negativity portrayed by Fine Gael and accused the party of employing negative clichés.
Mr Cowen was speaking during day one of a two-day Dáil debate on a motion of confidence in the Government.
The Government is expected to win tomorrow's vote comfortably.
Fine Gael leader Enda Kenny repeatedly challenged Mr Cowen to go to the country and said the people of the country have voted for a fresh start.
Labour leader Eamon Gilmore said the Government had lost its mandate and feared a General Election.
Sinn Féin's Caoimhghín Ó Caoláin said the 400,000 people in the dole queues meant the Coalition had to go.
Green Party leader John Gormley criticised the Opposition for not providing details on how they would fix the problems in the public finances if in power.
Dáil business had been cleared for today and tomorrow to allow time for the debate, which began after the order of business and Leaders' Questions to the Taoiseach.
The debate has adjourned and will resume in the morning. The vote on the motion is due at about 5.30pm tomorrow.
Today, the two new TDs - Independent Maureen O'Sullivan and Fine Gael's George Lee - took their seats in the Dáil.
Deputy Lee sat on the backbenches directly behind party leader Enda Kenny.
Faced with a Fine Gael motion of no confidence, the Government responded in the traditional way - meeting the challenge head-on by putting down its own confidence motion.
However, the Government looks set to have a comfortable six vote majority, with no signs of any of its supporters jumping ship.
Independent TD Michael Lowry met the Taoiseach this afternoon to discuss a number of matters of concern in advance of tomorrow's vote.
Government sources remain confident that he will continue to support the Government.
Deputy Lowry told RTÉ News that his support for the Government was always conditional on the delivery of a package to his constituency, and he wanted to discuss some of the projects involved with the Taoiseach.